Innovation policies seek to prepare an economy for the future by steering it on a transformation path to make it more competitive in increasingly global and interconnected markets. While most advanced economies have a tradition of strategymaking for territorially-based innovation and economic development, transition countries moving from centralised unaccountable planning to decentralised democratic policymaking have no working, market-based practices to build on. Governments in such contexts often resort to mimicking the economic priorities and instruments of advanced countries. We suggest a trajectory for transition countries to avoid the widespread pitfall of poorly defined innovation policies by upgrading and changing their industrial polices in line with the ideas embedded in the concept of innovation strategies for smart specialisation (RIS3): (1) Build a trusted 'competence centre' to provide a comprehensive analysis of your economic fabric and coordinate the process. (2) Begin with one strong economic domain in which engaged stakeholders work together with government bodies to define joint priorities and actions (domain experimentation). (3) Start with one region to experiment different approaches at subnational level (territorial experimentation). (4) Sequence your process in a way you can harvest the low-hanging fruits in the short-term (non-R&D measures), focus on the core of your activities with high potential in the medium term, and leave R&D-heavy breakthrough programmes for the longer term.